WIP: Refine toggling behaviour - [closed]

[tdowrick]

In GitLab by @AnastasisGeorgoulas on Aug 29, 2019, 17:22

Merges toggle-display -> load-image-files-rebased

Will address most of #80.

Main points:

• [x] Allow loading T2 MRI
• [x] Choose between two "views": neurostimulation or ultrasound
• [x] Update images directly on selection, without requiring Toggle button
• [x] Replace Visualise button functionality
• [x] Have slice viewers track neurostimulator probe when in that view
• [x] Show colourmap/diffusion appropriately when selected
• [ ] Choose which CT to show (from Stealth or from file)
• [ ] Prepare the segmentations so they display correctly (different colours, closed contours, opacity)
• [x] Show the appropriate volume/segmentations in the 3D viewer based on what view is chosen
• [x] Show outline of neurostimulation points in slice viewers

[tdowrick]

In GitLab by @AnastasisGeorgoulas on Aug 29, 2019, 17:54

added 2 commits

• b8433155 - Fix a bunch of linter complaints
• 7737d7a6 - Ignore one linter warning

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[tdowrick]

In GitLab by @AnastasisGeorgoulas on Aug 29, 2019, 18:04

added 1 commit

• ce60c37e - Add/remove empty lines not picked up by linter

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[tdowrick]

In GitLab by @AnastasisGeorgoulas on Sep 12, 2019, 14:28

added 1 commit

• 52fe08ee - Call this function correctly

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[tdowrick]

In GitLab by @AnastasisGeorgoulas on Sep 12, 2019, 15:03

added 2 commits

• 59c5cbd9 - Get image node correctly! (as loaded currently)
• 5ffe64cb - Don't show images in slice viewers on load

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[tdowrick]

In GitLab by @ThomasDowrick on Sep 23, 2019, 11:26

added 1 commit

• a5b80199 - Fix some display issues

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[tdowrick]

In GitLab by @AnastasisGeorgoulas on Sep 23, 2019, 11:33

added 1 commit

• ec3683f3 - Switch fg/bg for better visibility

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[tdowrick]

In GitLab by @AnastasisGeorgoulas on Oct 2, 2019, 18:05

added 7 commits

• a6d3f745 - Store all neurostim points for future manipulation
• 5443820e - Don't show neurostim point in US view at creation
• b001a6c3 - Show/hide neurostim points when switching view
• 6882d238 - Show/hide segmentations when switching view
• f97906d6 - Show/hide the reconstruction volume when switching
• 0a2349df - Simplify neurostim point selection
• 0ba034e1 - Fix visibility setting

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[tdowrick]

In GitLab by @AnastasisGeorgoulas on Oct 3, 2019, 07:58

added 6 commits

• 56ecbd6a - Add a convenience method to get the view
• b33d8fb9 - Show or hide the colourmap when box (un)checked
• 7834766d - Check colourmap status when switching view (wrong)
• b78d9fb3 - Fix so we always show the right image
• 8e1f1d4e - Remove some completed TODOs
• 765212f4 - Show selected image when switching to US view

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[tdowrick]

In GitLab by @AnastasisGeorgoulas on Oct 3, 2019, 07:58

marked the task Show colourmap/diffusion appropriately when selected as completed

[tdowrick]

In GitLab by @AnastasisGeorgoulas on Oct 3, 2019, 07:58

marked the task Show the appropriate volume/segmentations in the 3D viewer based on what view is chosen as completed

[tdowrick]

In GitLab by @AnastasisGeorgoulas on Oct 3, 2019, 08:14

Some things to note:

• This no longer uses the image loaded from the Stealth (called SLD-...). Instead, even in the US view, it will show whatever image is selected through the buttons (as long as it has been loaded from a file).
• I have checked that the layer changes work OK with saved images, but live data might be different. Specifically:
  • If the expected image (e.g. reconstruction) is not showing, first check that it is within bounds (in the main Slicer window, move the mouse inside the slice viewer - the main pane on the left should show the coordinates, and will show "Out of bounds" or something similar if the image in a layer is not in the box).
  • If something is outside bounds, it may be that we need to load the images centred (see this comment for how - this affects the load_data_from_file function in functions.py).
  • The Scout Scan and Reconstruction buttons that we have copied from PLUS Remote may be displaying the resulting volume (once the reconstruction is complete) in the wrong layer (background instead of foreground). If this happens, try reselecting the Ultrasound view; that should switch the layers in the right order. Alternatively, you can change them manually in the slice viewers, or it may be that the layer it chooses works better.
  • If all else fails, try changing the compositing mode in the slice viewers (it is a button with no tooltip, and an icon with a green and a yellow grid, between "Show reformat widget" and "Slice spacing may be...". ) For example, try switching from Alpha to Reverse Alpha or vice versa. We can do that programmatically once we find what works.
• It may be that segmentations are too opaque to show the neurostim points inside them/on their surface. If this happens, for now reduce the opacity through the Segmentations module, and then we can do this automatically in the Slicelet.

[tdowrick]

In GitLab by @AnastasisGeorgoulas on Oct 3, 2019, 16:38

added 2 commits

• 92d22c58 - Show neurostim point outlines in slices
• ff5bbd0b - Don't show segmentations if loading from US view

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[tdowrick]

In GitLab by @AnastasisGeorgoulas on Oct 3, 2019, 16:38

marked the task Show outline of neurostimulation points in slice viewers as completed

[tdowrick]

In GitLab by @AnastasisGeorgoulas on Oct 7, 2019, 11:46

added 2 commits

• 051380d2 - Send StylusToRas transform
• 1e5e2bab - Add some transparency to segmentations

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[tdowrick]

In GitLab by @RolandGuichard on Oct 8, 2019, 15:52

added 2 commits

• 001893b6 - Add an empty node
• 5b28360d - Add a button to set/unset the drivers in the slice nodes, ie changing from tracked to fixed mode

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[tdowrick]

In GitLab by @RolandGuichard on Oct 8, 2019, 16:03

added 1 commit

• 656b56c4 - Better warning message

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[tdowrick]

In GitLab by @RolandGuichard on Oct 8, 2019, 18:41

added 2 commits

• 0c7a22f7 - A new method to set the slice views in ultrasound live mode
• 12982182 - A new button to select and set up the ultrasound live mode

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[tdowrick]

In GitLab by @ThomasDowrick on Nov 22, 2019, 14:59

added 7 commits

• 09309b15 - Apply toggle_image and toggle_view once all transforms and MR loaded from...
• 7cb2feae - Rename model from Stealth from CT to MR
• 0071b38c - Add timer to keep 'Choose Image' box disabled until Live Recon has happened....
• edec4cc7 - collapse Local data box by default
• 9a15018e - Ultrasound view wasn't displaying the correct reslice view, fixed
• 0d66fcb3 - Don't hardcode TiptoTool transforms in PLUS Config
• b90939f1 - There was a redundant needle model to represent the BK model. Remove as we...

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[tdowrick]

In GitLab by @ThomasDowrick on Dec 9, 2019, 15:52

added 1 commit

• f18c2c6c - Create separate Slicelet just for pivot calibration. Can then update the...

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[tdowrick]

In GitLab by @ThomasDowrick on Dec 10, 2019, 09:33

added 1 commit

• d7545308 - Rename PLUS Config file used for Navigation, to make it more obvious what it is for

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[tdowrick]

In GitLab by @ThomasDowrick on Dec 10, 2019, 11:54

added 2 commits

• e3401e6b - Automatically set the Tool to Tip transforms in the XML config from the Pivot widget
• 248257e4 - Don't need the BK data when doing pivot calibration, so remove it from the PLUS config

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[tdowrick]

In GitLab by @ThomasDowrick on Jan 20, 2020, 15:54

closed